You will have to swap the input shaft and bearing retainer from the Fox T5 to the SN95 T5 if using the Fox bell housing. Or run the SN95 bellhousing which will move your shifter back a little and you might have to shorten the driveshaft (the SN95 input shaft is longer then the Fox, the SN95 bellhousing makes up for it. There are a lot of threads on all the different ways to do this and what people ran into.
A Tremec 3550/TKO/TKO 500/TKO 600 is a completely different transmission from a T5. Strong and almost bulletproof unless you run them without proper lubricant or full throttle shift without the clutch.
A Tremec T5 is still the same T5 that is prone to self destruction when used in a street/strip or racing environment
T5, all versions used in 5.0 Mustangs
Tremec 3550/TKO /TKO500/TKO600 AFTERMARKET replacement for T5 - handles racing environments with ease
On the tail shaft of the transmission, there will be a stamped aluminum tag. The tag will have a number on it that you can cross reference to the chart below. There is no other way to find out what type of T5 it is without disassembling it. All the rest of the numbers on the outside of the T5 case are part numbers which are not unique to any particular T5 model.
Remember that 94 - 97 T5's have a longer input shaft (about 11/16” longer) and can only be used with a 94-95 bell housing unless you modify or replace the input shaft.
T5's used with a 4 cylinder have a 3.93 first gear, reduced torque ratings and an input shaft pilot diameter that is smaller that the T5 used for V6 & V8 engines. The pilot diameter is .59" compared to the .668" used on V6 & V8 T5's. It requires a different pilot bearing to be used with a V6 or V8. The pilot bearing you need is for a Ford Ranger diesel from AutoZone part #14672
I don't know how you feel about the DYI thing when it comes to gears, some people don't like the idea of working on transmissions. If the DYI transmission fix idea isn't something that you would rather leave to someone else, here are some resources:
A T5 rebuild kit with syncros, bearings and other small parts costs about $160. It does not include any gears or shafts.
http://www.hanlonmotorsports.com/ also has a video on how to rebuild your T5 or Tremec. It costs about $20, and is worth every penny of it.
I did a Tremec 3550 rebuild, and it wasn't that difficult. The video was an immense help, and I would recommend viewing it. At $20, it will give you an opportunity to look and decide for yourself if you think that it is something you want to try to do.
T5 Shim kits – best product I have seen in a while… http://www.5speeds.com/t5/shims.html
“The Peel ‘n Place T5 World Class shim kit makes shimming T5 counter gear and main drive gears very easy.”